It has recently been demonstrated that small molecules (mw less than 800) have the potential to recover activity from proteins functionally impaired by genetic mutations. We have recently demonstrated that a subtype selective thyroid hormone analog could be rationally designed to bind to a mutant form of thyroid hormone receptor beta (hTRbeta) associated with the human disease RTH (resistance to thyroid hormone). These studies suggest that in principle, new therapeutics could be developed to a significant number of human genetic diseases if small molecules could be designed to complement mutational defects to proteins. This proposal explores the scope and limitations of using designed molecules to complement functionally impaired proteins involved in human disease. The nuclear hormone receptors, particularly TR mutants associated with RTH, are an ideal system to study because of the substantial structural and biochemical information that is available. In addition we can use known high-affinity ligands as scaffolds with which to explore molecular design. We will explore new strategies to design ligands that may restore function to RTH associated mutations of TRbeta that involve defects to, salt-bridge interactions, hydrogen bonds, hydrophobic packing, conformational switching and co-activator association. In addition, peptide conjugates will be used to explore methods with which compounds might compensate for mutations that result in protein truncations. The generality of our design strategies will be explored by designing molecular complements to similar mutations found in the vitamin D receptor (VDR) that are associated with rickets. We will also explore and further develop a new estrogen analog that selectively binds an estrogen receptor mutant that is does not appreciably bind estradiol. Modified ligands and mutants will be explored to improve the selectivity of this orthogonal transcriptional regulator. Applications of these compounds as biologically inert activators of conditional recombinases will also be explored.